-
1
-
-
0015980083
-
On earlier states of the biochemical system
-
Ycas M. On earlier states of the biochemical system. J. Theor. Biol. 44 (1974) 145-160
-
(1974)
J. Theor. Biol.
, vol.44
, pp. 145-160
-
-
Ycas, M.1
-
2
-
-
0017272554
-
Enzyme recruitment in evolution of new function
-
Jensen R.A. Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 30 (1976) 409-425
-
(1976)
Annu. Rev. Microbiol.
, vol.30
, pp. 409-425
-
-
Jensen, R.A.1
-
3
-
-
0033117461
-
Catalytic promiscuity and the evolution of new enzymatic activities
-
O'Brien P.J., and Herschlag D. Catalytic promiscuity and the evolution of new enzymatic activities. Chem. Biol. 6 (1999) R91-R105
-
(1999)
Chem. Biol.
, vol.6
-
-
O'Brien, P.J.1
Herschlag, D.2
-
4
-
-
0034923923
-
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies
-
Gerlt J.A., and Babbitt P.C. Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu. Rev. Biochem. 70 (2001) 209-246
-
(2001)
Annu. Rev. Biochem.
, vol.70
, pp. 209-246
-
-
Gerlt, J.A.1
Babbitt, P.C.2
-
5
-
-
0035846958
-
In vitro evolution of beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates
-
Matsumura I., and Ellington A.D. In vitro evolution of beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates. J. Mol. Biol. 305 (2001) 331-339
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 331-339
-
-
Matsumura, I.1
Ellington, A.D.2
-
7
-
-
0037396292
-
Enzymes with extra talents: moonlighting functions and catalytic promiscuity
-
Copley S.D. Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr. Opin. Chem. Biol. 7 (2003) 265-272
-
(2003)
Curr. Opin. Chem. Biol.
, vol.7
, pp. 265-272
-
-
Copley, S.D.1
-
8
-
-
0028342845
-
The evolution of functionally novel proteins after gene duplication
-
Hughes A.L. The evolution of functionally novel proteins after gene duplication. Proc. Biol. Sci. 256 (1994) 119-124
-
(1994)
Proc. Biol. Sci.
, vol.256
, pp. 119-124
-
-
Hughes, A.L.1
-
9
-
-
0034698298
-
One sequence, two ribozymes: implications for the emergence of new ribozyme folds
-
Schultes E.A., and Bartel D.P. One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science 289 (2000) 448-452
-
(2000)
Science
, vol.289
, pp. 448-452
-
-
Schultes, E.A.1
Bartel, D.P.2
-
10
-
-
11244281311
-
The 'evolvability' of promiscuous protein functions
-
Aharoni A., Gaidukov L., Khersonsky O., Mc Q.G.S., Roodveldt C., and Tawfik D.S. The 'evolvability' of promiscuous protein functions. Nature Genet. 37 (2005) 73-76
-
(2005)
Nature Genet.
, vol.37
, pp. 73-76
-
-
Aharoni, A.1
Gaidukov, L.2
Khersonsky, O.3
Mc, Q.G.S.4
Roodveldt, C.5
Tawfik, D.S.6
-
11
-
-
0038148710
-
Conformational diversity and protein evolution-a 60-year-old hypothesis revisited
-
James L.C., and Tawfik D.S. Conformational diversity and protein evolution-a 60-year-old hypothesis revisited. Trends Biochem. Sci. 28 (2003) 361-368
-
(2003)
Trends Biochem. Sci.
, vol.28
, pp. 361-368
-
-
James, L.C.1
Tawfik, D.S.2
-
12
-
-
9744279773
-
Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity
-
Gerlt J.A., Babbitt P.C., and Rayment I. Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity. Arch. Biochem. Biophys. 433 (2005) 59-70
-
(2005)
Arch. Biochem. Biophys.
, vol.433
, pp. 59-70
-
-
Gerlt, J.A.1
Babbitt, P.C.2
Rayment, I.3
-
13
-
-
0024289934
-
Crystal structure of enolase indicates that enolase and pyruvate kinase evolved from a common ancestor
-
Lebioda L., and Stec B. Crystal structure of enolase indicates that enolase and pyruvate kinase evolved from a common ancestor. Nature 333 (1988) 683-686
-
(1988)
Nature
, vol.333
, pp. 683-686
-
-
Lebioda, L.1
Stec, B.2
-
14
-
-
0025989437
-
Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5-Å resolution: identification of the active site and possible catalytic residues
-
Neidhart D.J., Howell P.L., Petsko G.A., Powers V.M., Li R.S., Kenyon G.L., and Gerlt J.A. Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5-Å resolution: identification of the active site and possible catalytic residues. Biochemistry 30 (1991) 9264-9273
-
(1991)
Biochemistry
, vol.30
, pp. 9264-9273
-
-
Neidhart, D.J.1
Howell, P.L.2
Petsko, G.A.3
Powers, V.M.4
Li, R.S.5
Kenyon, G.L.6
Gerlt, J.A.7
-
15
-
-
0028009918
-
The role of lysine 166 in the mechanism of mandelate racemase from Pseudomonas putida: mechanistic and crystallographic evidence for stereospecific alkylation by (R)-alpha-phenylglycidate
-
Landro J.A., Gerlt J.A., Kozarich J.W., Koo C.W., Shah V.J., Kenyon G.L., et al. The role of lysine 166 in the mechanism of mandelate racemase from Pseudomonas putida: mechanistic and crystallographic evidence for stereospecific alkylation by (R)-alpha-phenylglycidate. Biochemistry 33 (1994) 635-643
-
(1994)
Biochemistry
, vol.33
, pp. 635-643
-
-
Landro, J.A.1
Gerlt, J.A.2
Kozarich, J.W.3
Koo, C.W.4
Shah, V.J.5
Kenyon, G.L.6
-
16
-
-
0027964654
-
2+) complex of yeast enolase and the intermediate analog phosphonoacetohydroxamate at 2.1-Å resolution
-
2+) complex of yeast enolase and the intermediate analog phosphonoacetohydroxamate at 2.1-Å resolution. Biochemistry 33 (1994) 9333-9342
-
(1994)
Biochemistry
, vol.33
, pp. 9333-9342
-
-
Wedekind, J.E.1
Poyner, R.R.2
Reed, G.H.3
Rayment, I.4
-
18
-
-
0034712668
-
Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by d-glucarate dehydratase from Escherichia coli
-
Gulick A.M., Hubbard B.K., Gerlt J.A., and Rayment I. Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by d-glucarate dehydratase from Escherichia coli. Biochemistry 39 (2000) 4590-4602
-
(2000)
Biochemistry
, vol.39
, pp. 4590-4602
-
-
Gulick, A.M.1
Hubbard, B.K.2
Gerlt, J.A.3
Rayment, I.4
-
19
-
-
12644303230
-
The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids
-
Babbitt P.C., Hasson M.S., Wedekind J.E., Palmer D.R., Barrett W.C., Reed G.H., et al. The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids. Biochemistry 35 (1996) 16489-16501
-
(1996)
Biochemistry
, vol.35
, pp. 16489-16501
-
-
Babbitt, P.C.1
Hasson, M.S.2
Wedekind, J.E.3
Palmer, D.R.4
Barrett, W.C.5
Reed, G.H.6
-
21
-
-
0034677669
-
Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
-
Wilson C.A., Kreychman J., and Gerstein M. Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J. Mol. Biol. 297 (2000) 233-249
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 233-249
-
-
Wilson, C.A.1
Kreychman, J.2
Gerstein, M.3
-
22
-
-
0035815113
-
Evolution of function in protein superfamilies, from a structural perspective
-
Todd A.E., Orengo C.A., and Thornton J.M. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307 (2001) 1113-1143
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 1113-1143
-
-
Todd, A.E.1
Orengo, C.A.2
Thornton, J.M.3
-
23
-
-
0036308741
-
Enzyme function less conserved than anticipated
-
Rost B. Enzyme function less conserved than anticipated. J. Mol. Biol. 318 (2002) 595-608
-
(2002)
J. Mol. Biol.
, vol.318
, pp. 595-608
-
-
Rost, B.1
-
24
-
-
0142106373
-
How well is enzyme function conserved as a function of pairwise sequence identity?
-
Tian W., and Skolnick J. How well is enzyme function conserved as a function of pairwise sequence identity?. J. Mol. Biol. 333 (2003) 863-882
-
(2003)
J. Mol. Biol.
, vol.333
, pp. 863-882
-
-
Tian, W.1
Skolnick, J.2
-
25
-
-
0033528659
-
Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase
-
Palmer D.R., Garrett J.B., Sharma V., Meganathan R., Babbitt P.C., and Gerlt J.A. Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase. Biochemistry 38 (1999) 4252-4258
-
(1999)
Biochemistry
, vol.38
, pp. 4252-4258
-
-
Palmer, D.R.1
Garrett, J.B.2
Sharma, V.3
Meganathan, R.4
Babbitt, P.C.5
Gerlt, J.A.6
-
26
-
-
0346096856
-
Evolution of enzymatic activity in the enolase superfamily: functional studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis
-
Taylor Ringia E.A., Garrett J.B., Thoden J.B., Holden H.M., Rayment I., and Gerlt J.A. Evolution of enzymatic activity in the enolase superfamily: functional studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis. Biochemistry 43 (2004) 224-229
-
(2004)
Biochemistry
, vol.43
, pp. 224-229
-
-
Taylor Ringia, E.A.1
Garrett, J.B.2
Thoden, J.B.3
Holden, H.M.4
Rayment, I.5
Gerlt, J.A.6
-
27
-
-
0035219809
-
Biosynthesis of menaquinone (vitamin K2) and ubiquinone (coenzyme Q): a perspective on enzymatic mechanisms
-
Meganathan R. Biosynthesis of menaquinone (vitamin K2) and ubiquinone (coenzyme Q): a perspective on enzymatic mechanisms. Vitam. Horm. 61 (2001) 173-218
-
(2001)
Vitam. Horm.
, vol.61
, pp. 173-218
-
-
Meganathan, R.1
-
28
-
-
0019490792
-
Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication
-
Collins M.D., and Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol. Rev. 45 (1981) 316-354
-
(1981)
Microbiol. Rev.
, vol.45
, pp. 316-354
-
-
Collins, M.D.1
Jones, D.2
-
29
-
-
0035943351
-
The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli
-
Teichmann S.A., Rison S.C., Thornton J.M., Riley M., Gough J., and Chothia C. The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. J. Mol. Biol. 311 (2001) 693-708
-
(2001)
J. Mol. Biol.
, vol.311
, pp. 693-708
-
-
Teichmann, S.A.1
Rison, S.C.2
Thornton, J.M.3
Riley, M.4
Gough, J.5
Chothia, C.6
-
31
-
-
15944418238
-
Representing structure-function relationships in mechanistically diverse enzyme superfamilies
-
Pegg S.C., Brown S., Ojha S., Huang C.C., Ferrin T.E., and Babbitt P.C. Representing structure-function relationships in mechanistically diverse enzyme superfamilies. Pac. Symp. Biocomput. 10 (2005) 358-369
-
(2005)
Pac. Symp. Biocomput.
, vol.10
, pp. 358-369
-
-
Pegg, S.C.1
Brown, S.2
Ojha, S.3
Huang, C.C.4
Ferrin, T.E.5
Babbitt, P.C.6
-
32
-
-
33644560639
-
Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database
-
Pegg S.C., Brown S.D., Ojha S., Seffernick J., Meng E.C., Morris J.H., et al. Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry 45 (2006) 2545-2555
-
(2006)
Biochemistry
, vol.45
, pp. 2545-2555
-
-
Pegg, S.C.1
Brown, S.D.2
Ojha, S.3
Seffernick, J.4
Meng, E.C.5
Morris, J.H.6
-
33
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
Doolittle W.F. Phylogenetic classification and the universal tree. Science 284 (1999) 2124-2129
-
(1999)
Science
, vol.284
, pp. 2124-2129
-
-
Doolittle, W.F.1
-
34
-
-
0033043696
-
Is there a phylogenetic signal in prokaryote proteins?
-
Teichmann S.A., and Mitchison G. Is there a phylogenetic signal in prokaryote proteins?. J. Mol. Evol. 49 (1999) 98-107
-
(1999)
J. Mol. Evol.
, vol.49
, pp. 98-107
-
-
Teichmann, S.A.1
Mitchison, G.2
-
35
-
-
0036593395
-
Ancient phylogenetic relationships
-
Gribaldo S., and Philippe H. Ancient phylogenetic relationships. Theor. Popul. Biol. 61 (2002) 391-408
-
(2002)
Theor. Popul. Biol.
, vol.61
, pp. 391-408
-
-
Gribaldo, S.1
Philippe, H.2
-
36
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life
-
Delsuc F., Brinkmann H., and Philippe H. Phylogenomics and the reconstruction of the tree of life. Nature Rev. Genet. 6 (2005) 361-375
-
(2005)
Nature Rev. Genet.
, vol.6
, pp. 361-375
-
-
Delsuc, F.1
Brinkmann, H.2
Philippe, H.3
-
38
-
-
0348044549
-
Genome trees constructed using five different approaches suggest new major bacterial clades
-
Wolf Y.I., Rogozin I.B., Grishin N.V., Tatusov R.L., and Koonin E.V. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol. 1 (2001) 8
-
(2001)
BMC Evol. Biol.
, vol.1
, pp. 8
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Grishin, N.V.3
Tatusov, R.L.4
Koonin, E.V.5
-
39
-
-
0034942865
-
Universal trees based on large combined protein sequence data sets
-
Brown J.R., Douady C.J., Italia M.J., Marshall W.E., and Stanhope M.J. Universal trees based on large combined protein sequence data sets. Nature Genet. 28 (2001) 281-285
-
(2001)
Nature Genet.
, vol.28
, pp. 281-285
-
-
Brown, J.R.1
Douady, C.J.2
Italia, M.J.3
Marshall, W.E.4
Stanhope, M.J.5
-
40
-
-
10644230266
-
A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land
-
Battistuzzi F.U., Feijao A., and Hedges S.B. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol. Biol. 4 (2004) 44
-
(2004)
BMC Evol. Biol.
, vol.4
, pp. 44
-
-
Battistuzzi, F.U.1
Feijao, A.2
Hedges, S.B.3
-
42
-
-
15544380021
-
Prokaryotic phylogenies inferred from protein structural domains
-
Deeds E.J., Hennessey H., and Shakhnovich E.I. Prokaryotic phylogenies inferred from protein structural domains. Genome Res. 15 (2005) 393-402
-
(2005)
Genome Res.
, vol.15
, pp. 393-402
-
-
Deeds, E.J.1
Hennessey, H.2
Shakhnovich, E.I.3
-
43
-
-
14544295684
-
Weighted genome trees: refinements and applications
-
Gophna U., Doolittle W.F., and Charlebois R.L. Weighted genome trees: refinements and applications. J. Bacteriol. 187 (2005) 1305-1316
-
(2005)
J. Bacteriol.
, vol.187
, pp. 1305-1316
-
-
Gophna, U.1
Doolittle, W.F.2
Charlebois, R.L.3
-
44
-
-
0347752397
-
Evolution of enzymatic activity in the enolase superfamily: structural and mutagenic studies of the mechanism of the reaction catalyzed by o-succinylbenzoate synthase from Escherichia coli
-
Klenchin V.A., Taylor Ringia E.A., Gerlt J.A., and Rayment I. Evolution of enzymatic activity in the enolase superfamily: structural and mutagenic studies of the mechanism of the reaction catalyzed by o-succinylbenzoate synthase from Escherichia coli. Biochemistry 42 (2003) 14427-14433
-
(2003)
Biochemistry
, vol.42
, pp. 14427-14433
-
-
Klenchin, V.A.1
Taylor Ringia, E.A.2
Gerlt, J.A.3
Rayment, I.4
-
45
-
-
2442612271
-
Evolution of enzymatic activity in the enolase superfamily: structural studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis
-
Thoden J.B., Taylor Ringia E.A., Garrett J.B., Gerlt J.A., Holden H.M., and Rayment I. Evolution of enzymatic activity in the enolase superfamily: structural studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis. Biochemistry 43 (2004) 5716-5727
-
(2004)
Biochemistry
, vol.43
, pp. 5716-5727
-
-
Thoden, J.B.1
Taylor Ringia, E.A.2
Garrett, J.B.3
Gerlt, J.A.4
Holden, H.M.5
Rayment, I.6
-
46
-
-
0034812536
-
The lesser "burden borne" by o-succinylbenzoate synthase: an "easy" reaction involving a carboxylate carbon acid
-
Taylor E.A., Palmer D.R., and Gerlt J.A. The lesser "burden borne" by o-succinylbenzoate synthase: an "easy" reaction involving a carboxylate carbon acid. J. Am. Chem. Soc. 123 (2001) 5824-5825
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 5824-5825
-
-
Taylor, E.A.1
Palmer, D.R.2
Gerlt, J.A.3
-
47
-
-
0028871609
-
X-ray structure and catalytic mechanism of lobster enolase
-
Duquerroy S., Camus C., and Janin J. X-ray structure and catalytic mechanism of lobster enolase. Biochemistry 34 (1995) 12513-12523
-
(1995)
Biochemistry
, vol.34
, pp. 12513-12523
-
-
Duquerroy, S.1
Camus, C.2
Janin, J.3
-
48
-
-
0035955548
-
Crystal structure of the Escherichia coli RNA degradosome component enolase
-
Kuhnel K., and Luisi B.F. Crystal structure of the Escherichia coli RNA degradosome component enolase. J. Mol. Biol. 313 (2001) 583-592
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 583-592
-
-
Kuhnel, K.1
Luisi, B.F.2
-
49
-
-
3843145057
-
Expression, purification and the 1.8 angstroms resolution crystal structure of human neuron specific enolase
-
Chai G., Brewer J.M., Lovelace L.L., Aoki T., Minor W., and Lebioda L. Expression, purification and the 1.8 angstroms resolution crystal structure of human neuron specific enolase. J. Mol. Biol. 341 (2004) 1015-1021
-
(2004)
J. Mol. Biol.
, vol.341
, pp. 1015-1021
-
-
Chai, G.1
Brewer, J.M.2
Lovelace, L.L.3
Aoki, T.4
Minor, W.5
Lebioda, L.6
-
50
-
-
0042093706
-
The crystal structure of Trypanosoma brucei enolase: visualisation of the inhibitory metal binding site III and potential as target for selective, irreversible inhibition
-
da Silva Giotto M.T., Hannaert V., Vertommen D., de A. S. Navarro M.V., Rider M.H., Michels P.A., et al. The crystal structure of Trypanosoma brucei enolase: visualisation of the inhibitory metal binding site III and potential as target for selective, irreversible inhibition. J. Mol. Biol. 331 (2003) 653-665
-
(2003)
J. Mol. Biol.
, vol.331
, pp. 653-665
-
-
da Silva Giotto, M.T.1
Hannaert, V.2
Vertommen, D.3
de A. S. Navarro, M.V.4
Rider, M.H.5
Michels, P.A.6
-
51
-
-
0041810543
-
Crystal structure of Enterococcus hirae enolase at 2.8 Å resolution
-
Hosaka T., Meguro T., Yamato I., and Shirakihara Y. Crystal structure of Enterococcus hirae enolase at 2.8 Å resolution. J. Biochem. (Tokyo) 133 (2003) 817-823
-
(2003)
J. Biochem. (Tokyo)
, vol.133
, pp. 817-823
-
-
Hosaka, T.1
Meguro, T.2
Yamato, I.3
Shirakihara, Y.4
-
52
-
-
0034525463
-
Ribonucleotide reductases: the link between an RNA and a DNA world?
-
Stubbe J. Ribonucleotide reductases: the link between an RNA and a DNA world?. Curr. Opin. Struct. Biol. 10 (2000) 731-736
-
(2000)
Curr. Opin. Struct. Biol.
, vol.10
, pp. 731-736
-
-
Stubbe, J.1
-
53
-
-
2542504483
-
Structure, function, and mechanism of ribonucleotide reductases
-
Kolberg M., Strand K.R., Graff P., and Andersson K.K. Structure, function, and mechanism of ribonucleotide reductases. Biochim. Biophys. Acta 1699 (2004) 1-34
-
(2004)
Biochim. Biophys. Acta
, vol.1699
, pp. 1-34
-
-
Kolberg, M.1
Strand, K.R.2
Graff, P.3
Andersson, K.K.4
-
54
-
-
33645677238
-
Evolution of Enzymatic Activities in the Enolase Superfamily: N-Succinylamino Acid Racemase and a New Pathway for the Irreversible Conversion of D- to L-Amino Acids
-
Sakai A., Xiang D.F., Xu C., Song L., Yew W.S., Raushel F.M., and Gerlt J.A. Evolution of Enzymatic Activities in the Enolase Superfamily: N-Succinylamino Acid Racemase and a New Pathway for the Irreversible Conversion of D- to L-Amino Acids. Biochemistry 45 (2006) 4455-4462
-
(2006)
Biochemistry
, vol.45
, pp. 4455-4462
-
-
Sakai, A.1
Xiang, D.F.2
Xu, C.3
Song, L.4
Yew, W.S.5
Raushel, F.M.6
Gerlt, J.A.7
-
55
-
-
0029200309
-
The refined X-ray structure of muconate lactonizing enzyme from Pseudomonas putida PRS2000 at 1.85 Å resolution
-
Helin S., Kahn P.C., Guha B.L., Mallows D.G., and Goldman A. The refined X-ray structure of muconate lactonizing enzyme from Pseudomonas putida PRS2000 at 1.85 Å resolution. J. Mol. Biol. 254 (1995) 918-941
-
(1995)
J. Mol. Biol.
, vol.254
, pp. 918-941
-
-
Helin, S.1
Kahn, P.C.2
Guha, B.L.3
Mallows, D.G.4
Goldman, A.5
-
57
-
-
33745282893
-
-
Glasner, M. E., Gerlt, J. A. & Babbitt, P. C. (in press). Mechanisms of Protein Evolution and Their Application to Protein Engineering. In Advances in Enzymology and Related Areas of Molecular Biology (Toone, E., ed), Wiley and Sons, New York, NY.
-
-
-
-
58
-
-
0034682335
-
Lateral gene transfer and the nature of bacterial innovation
-
Ochman H., Lawrence J.G., and Groisman E.A. Lateral gene transfer and the nature of bacterial innovation. Nature 405 (2000) 299-304
-
(2000)
Nature
, vol.405
, pp. 299-304
-
-
Ochman, H.1
Lawrence, J.G.2
Groisman, E.A.3
-
59
-
-
0034780910
-
Horizontal gene transfer in prokaryotes: quantification and classification
-
Koonin E.V., Makarova K.S., and Aravind L. Horizontal gene transfer in prokaryotes: quantification and classification. Annu. Rev. Microbiol. 55 (2001) 709-742
-
(2001)
Annu. Rev. Microbiol.
, vol.55
, pp. 709-742
-
-
Koonin, E.V.1
Makarova, K.S.2
Aravind, L.3
-
60
-
-
0033670249
-
Horizontal gene transfer in bacterial and archaeal complete genomes
-
Garcia-Vallve S., Romeu A., and Palau J. Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res. 10 (2000) 1719-1725
-
(2000)
Genome Res.
, vol.10
, pp. 1719-1725
-
-
Garcia-Vallve, S.1
Romeu, A.2
Palau, J.3
-
61
-
-
0037471694
-
How big is the iceberg of which organellar genes in nuclear genomes are but the tip?
-
Doolittle W.F., Boucher Y., Nesbo C.L., Douady C.J., Andersson J.O., and Roger A.J. How big is the iceberg of which organellar genes in nuclear genomes are but the tip?. Phil. Trans. Roy. Soc. ser. B Biol. Sci. 358 (2003) 39-58
-
(2003)
Phil. Trans. Roy. Soc. ser. B Biol. Sci.
, vol.358
, pp. 39-58
-
-
Doolittle, W.F.1
Boucher, Y.2
Nesbo, C.L.3
Douady, C.J.4
Andersson, J.O.5
Roger, A.J.6
-
62
-
-
0037306453
-
Ancient horizontal gene transfer
-
Brown J.R. Ancient horizontal gene transfer. Nature Rev. Genet. 4 (2003) 121-132
-
(2003)
Nature Rev. Genet.
, vol.4
, pp. 121-132
-
-
Brown, J.R.1
-
63
-
-
0242354974
-
Horizontal gene transfer and phylogenetics
-
Philippe H., and Douady C.J. Horizontal gene transfer and phylogenetics. Curr. Opin. Microbiol. 6 (2003) 498-505
-
(2003)
Curr. Opin. Microbiol.
, vol.6
, pp. 498-505
-
-
Philippe, H.1
Douady, C.J.2
-
64
-
-
0034767491
-
Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence
-
Kennedy S.P., Ng W.V., Salzberg S.L., Hood L., and DasSarma S. Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Genome Res. 11 (2001) 1641-1650
-
(2001)
Genome Res.
, vol.11
, pp. 1641-1650
-
-
Kennedy, S.P.1
Ng, W.V.2
Salzberg, S.L.3
Hood, L.4
DasSarma, S.5
-
65
-
-
11844306574
-
The SEED: a peer-to-peer environment for genome annotation
-
Overbeek R., Disz T., and Stevens R. The SEED: a peer-to-peer environment for genome annotation. Communications of the ACM 47 (2004) 45-46
-
(2004)
Communications of the ACM
, vol.47
, pp. 45-46
-
-
Overbeek, R.1
Disz, T.2
Stevens, R.3
-
66
-
-
0019421477
-
Identification of Bacillus subtilis men mutants which lack O-succinylbenzoyl-coenzyme A synthetase and dihydroxynaphthoate synthase
-
Meganathan R., Bentley R., and Taber H. Identification of Bacillus subtilis men mutants which lack O-succinylbenzoyl-coenzyme A synthetase and dihydroxynaphthoate synthase. J. Bacteriol. 145 (1981) 328-332
-
(1981)
J. Bacteriol.
, vol.145
, pp. 328-332
-
-
Meganathan, R.1
Bentley, R.2
Taber, H.3
-
67
-
-
0019448757
-
Menaquinone biosynthesis in Bacillus subtilis: isolation of men mutants and evidence for clustering of men genes
-
Taber H.W., Dellers E.A., and Lombardo L.R. Menaquinone biosynthesis in Bacillus subtilis: isolation of men mutants and evidence for clustering of men genes. J. Bacteriol. 145 (1981) 321-327
-
(1981)
J. Bacteriol.
, vol.145
, pp. 321-327
-
-
Taber, H.W.1
Dellers, E.A.2
Lombardo, L.R.3
-
68
-
-
0026683420
-
Sequence organization and regulation of the Bacillus subtilis menBE operon
-
Driscoll J.R., and Taber H.W. Sequence organization and regulation of the Bacillus subtilis menBE operon. J. Bacteriol. 174 (1992) 5063-5071
-
(1992)
J. Bacteriol.
, vol.174
, pp. 5063-5071
-
-
Driscoll, J.R.1
Taber, H.W.2
-
69
-
-
0029584354
-
Structural organization of a Bacillus subtilis operon encoding menaquinone biosynthetic enzymes
-
Rowland B., Hill K., Miller P., Driscoll J., and Taber H. Structural organization of a Bacillus subtilis operon encoding menaquinone biosynthetic enzymes. Gene 167 (1995) 105-109
-
(1995)
Gene
, vol.167
, pp. 105-109
-
-
Rowland, B.1
Hill, K.2
Miller, P.3
Driscoll, J.4
Taber, H.5
-
70
-
-
0030992769
-
Identification of a novel gene cluster participating in menaquinone (vitamin K2) biosynthesis. Cloning and sequence determination of the 2-heptaprenyl-1,4-naphthoquinone methyltransferase gene of Bacillus stearothermophilus
-
Koike-Takeshita A., Koyama T., and Ogura K. Identification of a novel gene cluster participating in menaquinone (vitamin K2) biosynthesis. Cloning and sequence determination of the 2-heptaprenyl-1,4-naphthoquinone methyltransferase gene of Bacillus stearothermophilus. J. Biol. Chem. 272 (1997) 12380-12383
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 12380-12383
-
-
Koike-Takeshita, A.1
Koyama, T.2
Ogura, K.3
-
71
-
-
0034708819
-
Recruitment of a foreign quinone into the A(1) site of photosystem I. I. Genetic and physiological characterization of phylloquinone biosynthetic pathway mutants in Synechocystis sp. pcc 6803
-
Johnson T.W., Shen G., Zybailov B., Kolling D., Reategui R., Beauparlant S., et al. Recruitment of a foreign quinone into the A(1) site of photosystem I. I. Genetic and physiological characterization of phylloquinone biosynthetic pathway mutants in Synechocystis sp. pcc 6803. J. Biol. Chem. 275 (2000) 8523-8530
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 8523-8530
-
-
Johnson, T.W.1
Shen, G.2
Zybailov, B.3
Kolling, D.4
Reategui, R.5
Beauparlant, S.6
-
72
-
-
0032843908
-
Shotgun: getting more from sequence similarity searches
-
Pegg S.C., and Babbitt P.C. Shotgun: getting more from sequence similarity searches. Bioinformatics 15 (1999) 729-740
-
(1999)
Bioinformatics
, vol.15
, pp. 729-740
-
-
Pegg, S.C.1
Babbitt, P.C.2
-
73
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25 (1997) 3389-3402
-
(1997)
Nucl. Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
74
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl. Acids Res. 32 (2004) 1792-1797
-
(2004)
Nucl. Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
75
-
-
0037460952
-
MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance
-
Jewett A.I., Huang C.C., and Ferrin T.E. MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance. Bioinformatics 19 (2003) 625-634
-
(2003)
Bioinformatics
, vol.19
, pp. 625-634
-
-
Jewett, A.I.1
Huang, C.C.2
Ferrin, T.E.3
-
76
-
-
4444221565
-
UCSF Chimera-a visualization system for exploratory research and analysis
-
Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., and Ferrin T.E. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25 (2004) 1605-1612
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
77
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
-
(2003)
Bioinformatics
, vol.19
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
78
-
-
1342309210
-
Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
-
Altekar G., Dwarkadas S., Huelsenbeck J.P., and Ronquist F. Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20 (2004) 407-415
-
(2004)
Bioinformatics
, vol.20
, pp. 407-415
-
-
Altekar, G.1
Dwarkadas, S.2
Huelsenbeck, J.P.3
Ronquist, F.4
-
79
-
-
0035031966
-
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
-
Whelan S., and Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18 (2001) 691-699
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 691-699
-
-
Whelan, S.1
Goldman, N.2
-
80
-
-
33745285272
-
-
Felsenstein, J. (2004). PHYLIP (Phylogeny Inference Package) version 3.6. Department of Genome Science, University of Washington, Seattle.
-
-
-
-
81
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones D.T., Taylor W.R., and Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8 (1992) 275-282
-
(1992)
Comput. Appl. Biosci.
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
82
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Shindyalov I.N., and Bourne P.E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 11 (1998) 739-747
-
(1998)
Protein Eng.
, vol.11
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
84
-
-
11144354360
-
Environmental genome shotgun sequencing of the Sargasso Sea
-
Venter J.C., Remington K., Heidelberg J.F., Halpern A.L., Rusch D., Eisen J.A., et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304 (2004) 66-74
-
(2004)
Science
, vol.304
, pp. 66-74
-
-
Venter, J.C.1
Remington, K.2
Heidelberg, J.F.3
Halpern, A.L.4
Rusch, D.5
Eisen, J.A.6
|